Image-Based Modeling Reveals Dynamic Redistribution of DNA Damage into Nuclear Sub-Domains

Abstract

Several proteins involved in the response to DNA double strand breaks (DSB) form microscopically visible nuclear domains, or foci, after exposure to ionizing radiation. Radiation-induced foci (RIF) are believed to be located where DNA damage occurs. To test this assumption, we analyzed the spatial distribution of 53BP1, phosphorylated ATM, and γH2AX RIF in cells irradiated with high linear energy transfer (LET) radiation and low LET. Since energy is randomly deposited along high-LET particle paths, RIF along these paths should also be randomly distributed. The probability to induce DSB can be derived from DNA fragment data measured experimentally by pulsed-field gel electrophoresis. We used this probability in Monte Carlo simulations to predict DSB locations in synthetic nuclei geometrically described by a complete set of human chromosomes, taking into account microscope optics from real experiments. As expected, simulations produced DNA-weighted random (Poisson) distributions. In contrast, the distributions of RIF obtained as early as 5 min after exposure to high LET (1 GeV/amu Fe) were non-random. This deviation from the expected DNA-weighted random pattern can be further characterized by “relative DNA image measurements.” This novel imaging approach shows that RIF were located preferentially at the interface between high and low DNA density regions, and were more frequent than predicted in regions with lower DNA density. The same preferential nuclear location was also measured for RIF induced by 1 Gy of low-LET radiation. This deviation from random behavior was evident only 5 min after irradiation for phosphorylated ATM RIF, while γH2AX and 53BP1 RIF showed pronounced deviations up to 30 min after exposure. These data suggest that DNA damage–induced foci are restricted to certain regions of the nucleus of human epithelial cells. It is possible that DNA lesions are collected in these nuclear sub-domains for more efficient repair. DNA damages are daily cellular events. If such events are left unchecked in an organism, they can lead to DNA mutations and possibly cancer over a long period of time. Consequently, cells have very efficient DNA repair machinery. Many studies have focused on the different molecular factors involved in the repair machinery, neglecting to consider the spatial context where damage occurs. Therefore, little is known about the role the nuclear architecture might have in the DNA damage response. In this study, we introduce computer modeling and image analysis tools in order to relate the position of DNA damage markers to morphologically distinct regions of the nucleus. Using these tools, we show that radiation-induced damages locate preferentially in non-condensed DNA regions or at the boundary of regions with condensed DNA. These results contradict the current dogma that the molecular response to randomly generated DNA damages is independent of their nuclear locations. Instead, this suggests the existence of repair centers in the nucleus. Overall, our approach shows that nuclear architecture plays a role in the DNA damage response, reminding us that the nucleus is not simply a soup of DNA and proteins.